|
| Status |
Public on Aug 19, 2020 |
| Title |
BD_4C_Dnmt3aMatKO_RNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
BD_4C_Dnmt3aMatKO_RNA
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J x DBA/2J F1 hybrid
developmental stage: 4 cell embryo
genotype/variation: Dnmt3a2lox;Zp3-cre x WT
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cumulus cells were removed using hyaluronidase after insemination and embryos were cultured in KSOM at 37oC and 5% CO2. Total RNA was extracted from 5-10 pooled 4 cell embryos using Trizol reagent.
Strand-specific RNA-seq libraries were generated using NEBNext: rRNA Depletion Kit, RNA First Strand Synthesis Module, Ultra Directional RNA Second Strand Synthesis Module, and Ultra II DNA Library Prep Kit. Libraries were sequenced on HiSeq 1500 or HiSeq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
strand-specific RNAseq
|
| Data processing |
Reads were trimmed using Trimmomatic v0.32
Trimmed reads were aligned to the mm10 reference genome and a diploid pseudogenome using MEA and default parameters (Richard Albert et al. 2018)
RNA-seq: PCR duplicates and multi-aligned reads (q<255) were filtered out using Picard tools v1.92 and samtools v1.1
WGBS: PCR duplicates were filtered out using Picard tools v1.92 and samtools v1.1
Aligned read maps were converted to Wiggle format using bedtools v2.22.1 and bedGraphToBigWig (UCSC).
RNA-seq: total and allele-specific tracks were normalized by the number of uniquely aligned total reads
Genome_build: mm10
Supplementary_files_format_and_content: 3x bigWigs (total, maternal, paternal)
|
| |
|
| Submission date |
Dec 11, 2019 |
| Last update date |
Aug 19, 2020 |
| Contact name |
Matthew Lorincz |
| Organization name |
University of British Columbia
|
| Department |
Medical Genetics
|
| Lab |
Lorincz
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE141877 |
Maternal DNMT3A-dependent de novo methylation of the zygotic paternal genome inhibits gene expression in the early embryo |
|
| Relations |
| BioSample |
SAMN13543290 |
| SRA |
SRX7351062 |
